def test_get_num_fragments(self):
molecule = Molecule()
# get_num_fragments() should return 0 before any fragments added to molecule
self.assertEqual(molecule.get_num_fragments(), 0)
fragment0 = Fragment(1, 2)
atom0 = Atom("F", 0, 0, 0)
fragment0.add_atom(atom0)
molecule.add_fragment(fragment0)
# get_num_fragments() should return 1 after 1 fragment added to molecule
self.assertEqual(molecule.get_num_fragments(), 1)
fragment1 = Fragment(3, 2)
atom1 = Atom("F", 0, 0, 3)
atom2 = Atom("Cl", 0, 0, 0)
fragment1.add_atom(atom1)
fragment1.add_atom(atom2)
molecule.add_fragment(fragment1)
# get_num_fragments() should return 2 after 2 fragment added to molecule
self.assertEqual(molecule.get_num_fragments(), 2)
def get_missing_energy(self):
"""
Returns a single Calculation object, which contains the info a user needs to calculate an energy missing in the table.
The user should calculate the energy, then call either set_energy() or set_failed()
Args:
None
Returns:
A Calculation object describing the calculation to be performed
"""
# retrieve a pending job from the Jobs table
try:
job_id = self.cursor.execute(
"SELECT ROWID FROM Jobs WHERE status=?",
("pending", )).fetchone()[0]
except TypeError:
# this error will be thrown if there are no more energies to calculate, because None[0] throws a TypeError
return None
# retrieve the calculation and energy to be calculated for this job from the Energies table
calculation_id, energy_index = self.cursor.execute(
"SELECT calculation_id, energy_index FROM Energies WHERE job_id=?",
(job_id, )).fetchone()
# retrieve the molecule and model from the Calculations table
molecule_id, model_id, tag, optimized = self.cursor.execute(
"SELECT molecule_id, model_id, tag, optimized FROM Calculations WHERE ROWID=?",
(calculation_id, )).fetchone()
# retrieve the method, basis, and cp for this model
method, basis, cp = self.cursor.execute(
"SELECT method, basis, cp FROM Models WHERE ROWID=?",
(model_id, )).fetchone()
# Reconstruct the molecule from the information in this database
molecule = Molecule()
# loop over all rows in the Fragments table that correspond to this molecule
for fragment_id, charge, spin in self.cursor.execute(
"SELECT ROWID, charge, spin FROM Fragments WHERE molecule_id=?",
(molecule_id, )).fetchall():
fragment = Fragment(charge, spin)
# loop over all rows in the Atoms table that correspond to this fragment
for symbol, x, y, z in self.cursor.execute(
"SELECT symbol, x, y, z FROM Atoms WHERE fragment_id=?",
(fragment_id, )).fetchall():
fragment.add_atom(Atom(symbol, x, y, z))
molecule.add_fragment(fragment)
# get the indicies of the fragments to include in this calculation
fragment_indicies = energy_index_to_fragment_indicies(
energy_index, molecule.get_num_fragments())
# update the job with its start date and running status
self.cursor.execute(
"UPDATE Jobs SET status=?, start_date=? WHERE ROWID=?",
("running", datetime.datetime.today().strftime('%Y/%m/%d'),
job_id))
return Calculation(molecule, method, basis, True if cp == 1 else False,
fragment_indicies, job_id)
